Posts by anchal

... I could solve the problem...
Actually the problem was with BWA version I was using to align data (otherwise data quality was very good). Same data when aligned with BWA 0.5.9 gave very bad empirical scores whereas when aligned with 0.6.1 gave perfectly fine results. So be careful while using the ali ...

... I am analyzing exome sequencing data (~100x coverage). Pipeline includes BWA for alignment and then GATK for variation calling. While BQSR (one fthe steps in variation calling), the empirical base quality score values generated for my data are coming out to be very low. (I am looking at the average ...

... Hi all
I am using Unified Genotyper of (GATK) to call variations from my exome dataset. Before calling variations I realigned and recalibrated the dataset as suggested by GATK pipeline. Surprisingly for one of the samples unified genotyper is running for required time and ends without any error BUT ...

... Hi All
I have done exome sequencing for 6 samples. Now I am calling variations using GATK. I am calling variations for each sample individually and using all the sites across the genome (dbSNP_135. vcf file). also running vqsr on the same data for single sample and all the training sets as mentione ...